I have searched, and it appears as though there are similar bugs to this in past versions. Wordy explanation as I don't have coordinates to work with.

I'm playing in a realm in 1.0.0. The original portal (portal A) I'd built is near the world spawn point. There were no fortresses within a large radius of the portal so I built another one in the overworld, quite far away (portal B). This was about a 3 min powered minecart ride away, so a substantial distance. Portal B connected to the same original one in the nether. When I warped back through from the nether, I emerged at Portal A. I then took one block out of Portal A, and traveled back to Portal B. I went to the nether, emerged at the same point, and traveled back through the portal again - only to emerge at a new portal, near my spawn point but not exactly close to the old one (Portal C). I destroyed portal C and traveled about 2 minutes by powered minecart in the other direction. I made sure to set a new portal up (Portal D) with a different orientation than the others (E-W instead of north south). I emerged at the same portal in the nether and warped back to Portal A.

I'd expect that, like with other versions, different locations in the overworld should yield different locations in the nether.